Alignments for a candidate for pcaB in Brucella microti CCM 4915

GapMind for catabolism of small carbon sources

Alignments for a candidate for pcaB in Brucella microti CCM 4915

Align 3-Carboxy-cis,cis-muconate cycloisomerase (EC 5.5.1.2) (characterized)
to candidate WP_015799889.1 BMI_RS13080 3-carboxy-cis,cis-muconate cycloisomerase

Query= BRENDA::Q2HNZ1
         (353 letters)



>NCBI__GCF_000022745.1:WP_015799889.1
          Length = 354

 Score =  384 bits (985), Expect = e-111
 Identities = 208/352 (59%), Positives = 242/352 (68%), Gaps = 4/352 (1%)

Query: 1   MSLSPFEHPFLSGLFGDSE-IIELFSAKADIDAMIRFETALAQAEAEASIFADDEAEAIV 59
           MS+S FEHPFL+GLFGD E I  LF+A ADI AM++FE ALA A+A+  I     AE I+
Sbjct: 1   MSISVFEHPFLTGLFGDDEEISSLFTAYADIAAMLKFEAALAGAQADLGIIPAHAAERIM 60

Query: 60  SGLSEFAADMSALRHGVAKDGVVVPELIRQMRAAVAGQGADKVHFGATSQDVIDTSLMLR 119
           S       D++ L HG A+DGVVVP L+R +R  V    A  VHFGATSQDVIDTSLMLR
Sbjct: 61  SATETMEPDLAQLEHGTARDGVVVPALVRNLRKTVGEDVAAHVHFGATSQDVIDTSLMLR 120

Query: 120 LKMAAEIIATRLGHLIDTLGDLASRDGHKPLTGYTRMQAAIGITVADRAAGWIAPLERHL 179
           L    +I+  R+  L +    L +  G   LT YTRMQ AI  TVADR   W AP   + 
Sbjct: 121 LARVRDILVARIEQLSERFNWLETTFGQNDLTAYTRMQPAISTTVADRVESWRAPFSDYA 180

Query: 180 LRLETFAQNGFALQFGGAAGTLEKLGDNAGAVRADLAKRLGLADRPQWHNQRDGIPEFAN 239
            RL       F LQFGGAAGTLEK       +RA+LAKRLGL DRPQWH+QR  I +F +
Sbjct: 181 QRLAALQ---FPLQFGGAAGTLEKFVGKGAKLRAELAKRLGLEDRPQWHSQRAFIADFGH 237

Query: 240 LLSLVTGTLGKFGQDIALMAEIGSEIRLSGGGGSSAMPHKQNPVNAETLVTLARFNAVQI 299
           LLSLVTG+LGKFGQDIALMAE+  EI LSGGGGSSAMPHKQNPV AE LVTLARFNAVQ+
Sbjct: 238 LLSLVTGSLGKFGQDIALMAELRDEISLSGGGGSSAMPHKQNPVRAELLVTLARFNAVQV 297

Query: 300 SALHQSLVQEQERSGAGWMLEWLTLPQMVTATGTSLLVAERLAAQIDRLGAD 351
           S LHQ++V EQERSG  WMLEW+ LP +V ATG +L  A  L+  I R+G D
Sbjct: 298 SGLHQAMVHEQERSGTAWMLEWMILPPVVAATGAALKAALVLSENIVRMGKD 349


Lambda     K      H
   0.318    0.133    0.376 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 435
Number of extensions: 11
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 353
Length of database: 354
Length adjustment: 29
Effective length of query: 324
Effective length of database: 325
Effective search space:   105300
Effective search space used:   105300
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_015799889.1 BMI_RS13080 (3-carboxy-cis,cis-muconate cycloisomerase)
to HMM TIGR02426 (pcaB: 3-carboxy-cis,cis-muconate cycloisomerase (EC 5.5.1.2))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR02426.hmm
# target sequence database:        /tmp/gapView.2803538.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02426  [M=338]
Accession:   TIGR02426
Description: protocat_pcaB: 3-carboxy-cis,cis-muconate cycloisomerase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-141  457.0   8.2   1.9e-141  456.8   8.2    1.0  1  NCBI__GCF_000022745.1:WP_015799889.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000022745.1:WP_015799889.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  456.8   8.2  1.9e-141  1.9e-141       1     338 []      10     343 ..      10     343 .. 0.99

  Alignments for each domain:
  == domain 1  score: 456.8 bits;  conditional E-value: 1.9e-141
                             TIGR02426   1 lldglfgdse.aaelfsdrarlramldvEaalaraqadvGlipaeaaeaiaaaaaelalDlealaeaaaeagn 72 
                                           +l+glfgd+e +++lf+++a+++aml++Eaala aqad+G+ipa+aae+i++a++++++Dl++l++++a++g+
  NCBI__GCF_000022745.1:WP_015799889.1  10 FLTGLFGDDEeISSLFTAYADIAAMLKFEAALAGAQADLGIIPAHAAERIMSATETMEPDLAQLEHGTARDGV 82 
                                           67899*99877************************************************************** PP

                             TIGR02426  73 vviplvkalrkavaeeaaryvHlGaTSQDviDTalmLqlrdaldllladlerlaeaLaelaarhrdtpltarT 145
                                           vv+ lv++lrk+v+e++a++vH+GaTSQDviDT+lmL+l++++d+l+a++e+l+e++++l++++++++lta+T
  NCBI__GCF_000022745.1:WP_015799889.1  83 VVPALVRNLRKTVGEDVAAHVHFGATSQDVIDTSLMLRLARVRDILVARIEQLSERFNWLETTFGQNDLTAYT 155
                                           ************************************************************************* PP

                             TIGR02426 146 llQqAvpttvglkaagwlaavlrardrlealrtealalqfGGAaGtlaalekkglavaealAaelgLeapalp 218
                                           ++Q+A++ttv++++++w+a+++++++rl+al+   ++lqfGGAaGtl+++  kg +++++lA++lgLe+ + +
  NCBI__GCF_000022745.1:WP_015799889.1 156 RMQPAISTTVADRVESWRAPFSDYAQRLAALQ---FPLQFGGAAGTLEKFVGKGAKLRAELAKRLGLED-RPQ 224
                                           ********************************...**************999999**************.*** PP

                             TIGR02426 219 WhtqrdriaelaaaLalvagalgkiaqDvallaqtevgevleaggGGSSampHKrNPvaaevlaaaarrapgl 291
                                           Wh+qr++ia+++++L+lv+g+lgk++qD+al+a+++ +++l+ ggGGSSampHK+NPv+ae+l+++ar+++++
  NCBI__GCF_000022745.1:WP_015799889.1 225 WHSQRAFIADFGHLLSLVTGSLGKFGQDIALMAELRDEISLS-GGGGSSAMPHKQNPVRAELLVTLARFNAVQ 296
                                           *****************************************9.99**************************** PP

                             TIGR02426 292 vatLfaalaqedeRsaggWhaeWetLrelvaltagalrqaaellegl 338
                                           v++L++a+++e+eRs+++W++eW++L+ +va+t++al++a +l+e++
  NCBI__GCF_000022745.1:WP_015799889.1 297 VSGLHQAMVHEQERSGTAWMLEWMILPPVVAATGAALKAALVLSENI 343
                                           *****************************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (338 nodes)
Target sequences:                          1  (354 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 14.32
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources